Fix setup

[rtibbles]

Summary

Description of the change(s) you made

Setup does not run since the Django 3.2 upgrade
Tighter SQLite foreign key constraints made this issue surface
Fixes this by handling integrity errors in setting prerequisite relationships and by not setting root nodes as incomplete in the mark_incomplete command.

Should at least provide more diagnostic errors for #3234 if it does not fix it

Manual verification steps performed

1. Ran ./contentcuration/manage.py setup it did not break!

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[sairina]

lgtm! Everything seems to be fixed. Thank you!

[bjester]

Ah that's how to do it with a multi-line arguments list

[rtibbles]

It took me a couple of tries...